8VDV | pdb_00008vdv

pcsk9 in complex with inhibitor

PDB DOI: https://doi.org/10.2210/pdb8VDV/pdb

Classification: HYDROLASE/INHIBITOR
Organism(s): Homo sapiens, synthetic construct
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-12-18 Released: 2025-03-26
Deposition Author(s): Xu, M., Chopra, R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.217 (Depositor), 0.219 (DCC)
R-Value Work:
0.186 (Depositor), 0.191 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

PCSK9 in complex with inhibitor

Xu, M., Xu, M.

To be published.

Macromolecule Content

Total Structure Weight: 67.83 kDa
Atom Count: 4,633
Modeled Residue Count: 581
Deposited Residue Count: 632
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proprotein convertase subtilisin/kexin type 9	A	92	Homo sapiens	Mutation(s): 0 Gene Names: PCSK9, NARC1, PSEC0052 EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBP7 (Homo sapiens) Explore Q8NBP7 Go to UniProtKB: Q8NBP7
PHAROS: Q8NBP7 GTEx: ENSG00000169174
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NBP7
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proprotein convertase subtilisin/kexin type 9	B	529	Homo sapiens	Mutation(s): 0 Gene Names: PCSK9, NARC1, PSEC0052 EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBP7 (Homo sapiens) Explore Q8NBP7 Go to UniProtKB: Q8NBP7
PHAROS: Q8NBP7 GTEx: ENSG00000169174
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8NBP7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Inhibitor YBX-PHE-VAL-GLY-THR-THR-PHA-MAA-BIF-EME-NEH	C [auth L]	11	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues 4 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BIF Query on BIF	C [auth L]	L-PEPTIDE LINKING	C₁₅ H₁₅ N O₂		PHE
EME Query on EME	C [auth L]	L-PEPTIDE LINKING	C₆ H₁₁ N O₄		GLU
MAA Query on MAA	C [auth L]	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
PHA Query on PHA	C [auth L]	L-PEPTIDE LINKING	C₉ H₁₁ N O		PHE

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002534 Query on PRD_002534	C [auth L]	Inhibitor YBX-PHE-VAL-GLY-THR-THR-PHA-MAA-BIF-EME-NEH	Cyclic peptide / Inhibitor		Interactions Focus chain C [auth L] Interactions & Density Focus chain C [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.217 (Depositor), 0.219 (DCC)
R-Value Work: 0.186 (Depositor), 0.191 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.086	α = 90
b = 70.846	β = 90
c = 149.007	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-03-26
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.